Merge branch 'skipfluxcal'

sdss · Jan 19, 2024 · a031564 · a031564
2 parents d2c24c8 + 4332642
commit a031564
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Showing 3 changed files with 24 additions and 12 deletions.
diff --git a/bin/drp b/bin/drp
@@ -115,12 +115,13 @@ cli.add_command(metacli)
 @click.option('-f', '--use-fiducial-master', is_flag=True, default=False, help='use fiducial master calibration frames')
 @click.option('-s', '--skip-sky-subtraction', is_flag=True, help='skip sky subtraction')
 @click.option('--sky-weights', type=(float, float), default=None, help='weights (east, west) for the master sky combination')
+@click.option('-c', '--skip-flux-calibration', is_flag=True, default=False, help='skip flux calibration')
 @click.option('-n', '--ncpus', type=int, default=None, help='number of CPUs to use during extraction')
 @click.option("-a", "--aperture-extraction", is_flag=True, default=False, help="run quick reduction with aperture extraction")
 def quick_reduction(expnum: int, use_fiducial_master: bool, skip_sky_subtraction: bool,
-                    sky_weights: tuple, ncpus: int, aperture_extraction: bool) -> None:
+                    sky_weights: tuple, skip_flux_calibration: bool, ncpus: int, aperture_extraction: bool) -> None:
     quick_science_reduction(expnum, use_fiducial_master, skip_sky_subtraction,
-                            sky_weights, ncpus, aperture_extraction)
+                            sky_weights, skip_flux_calibration, ncpus, aperture_extraction)
 
 
 # register quick DRP command

diff --git a/python/lvmdrp/functions/fluxCalMethod.py b/python/lvmdrp/functions/fluxCalMethod.py
@@ -66,8 +66,7 @@
     "correctTelluric_drp",
 ]
 
-
-def apply_fluxcal(in_rss: str, out_rss: str, display_plots: bool = False):
+def apply_fluxcal(in_rss: str, out_rss: str, skip_fluxcal: bool = False, display_plots: bool = False):
     """applies flux calibration to spectrograph-combined data
 
     Parameters
@@ -76,6 +75,8 @@ def apply_fluxcal(in_rss: str, out_rss: str, display_plots: bool = False):
         input RSS file
     out_rss : str
         output RSS file
+    skip_fluxcal : bool, optional
+        whether to skip flux calibration, by default False
     display_plots : bool, optional
 
     Returns
@@ -123,7 +124,7 @@ def apply_fluxcal(in_rss: str, out_rss: str, display_plots: bool = False):
     sens_ave = biweight_location(sens_arr, axis=1, ignore_nan=True)
     sens_rms = biweight_scale(sens_arr, axis=1, ignore_nan=True)
 
-    # fix all zeros
+    # fix case of all invalid values
     if (sens_ave == 0).all() or np.isnan(sens_ave).all():
         log.warning(
             "all sensitivity values are zero or NaN, impossible to flux-calibrate"
@@ -168,12 +169,21 @@ def apply_fluxcal(in_rss: str, out_rss: str, display_plots: bool = False):
     ext = np.interp(rss._wave, lext, ext)
     sci_secz = rss._header["TESCIAM"]
 
-    log.info("flux-calibrating data science and sky spectra")
-
-    rss._data *= sens_ave * 10 ** (0.4 * ext * (sci_secz)) / exptimes[:, None]
-    rss._error *= sens_ave * 10 ** (0.4 * ext * (sci_secz)) / exptimes[:, None]
-    rss._sky *= sens_ave * 10 ** (0.4 * ext * (sci_secz)) / exptimes[:, None]
-    rss._sky_error *= sens_ave * 10 ** (0.4 * ext * (sci_secz)) / exptimes[:, None]
+    # optionally sky flux calibration
+    if skip_fluxcal:
+        log.info("skipping flux calibration")
+        rss._data /= exptimes[:, None]
+        rss._error /= exptimes[:, None]
+        rss._sky /= exptimes[:, None]
+        rss._sky_error /= exptimes[:, None]
+        rss.setHdrValue("FLUXCAL", False, "flux-calibrated?")
+        rss.setHdrValue("BUNIT", "electron/s/A", "flux units")
+    else:
+        log.info("flux-calibrating data science and sky spectra")
+        rss._data *= sens_ave * 10 ** (0.4 * ext * (sci_secz)) / exptimes[:, None]
+        rss._error *= sens_ave * 10 ** (0.4 * ext * (sci_secz)) / exptimes[:, None]
+        rss._sky *= sens_ave * 10 ** (0.4 * ext * (sci_secz)) / exptimes[:, None]
+        rss._sky_error *= sens_ave * 10 ** (0.4 * ext * (sci_secz)) / exptimes[:, None]
 
     log.info(f"writing output file in {os.path.basename(out_rss)}")
     rss.writeFitsData(out_rss)

diff --git a/python/lvmdrp/functions/run_quickdrp.py b/python/lvmdrp/functions/run_quickdrp.py
@@ -119,6 +119,7 @@ def get_master_mjd(sci_mjd: int) -> int:
 def quick_science_reduction(expnum: int, use_fiducial_master: bool = False,
                             skip_sky_subtraction: bool = False,
                             sky_weights: Tuple[float, float] = None,
+                            skip_flux_calibration: bool = False,
                             ncpus: int = None,
                             aperture_extraction: bool = False) -> None:
     """ Run the Quick DRP for a given exposure number.
@@ -275,7 +276,7 @@ def quick_science_reduction(expnum: int, use_fiducial_master: bool = False,
     sci_paths = sorted(drp.path.expand("lvm_anc", drpver=drpver, tileid=sci_tileid, mjd=sci_mjd, kind="", imagetype="object", camera="*", expnum=sci_expnum))
     sci_paths = [sci_path for sci_path in sci_paths if "lvm-object-sp" not in sci_path]
     for sci_path in sci_paths:
-        flux_tasks.apply_fluxcal(in_rss=sci_path, out_rss=sci_path)
+        flux_tasks.apply_fluxcal(in_rss=sci_path, out_rss=sci_path, skip_fluxcal=skip_flux_calibration)
 
     # combine channels
     drp.combine_channels(tileid=sci_tileid, mjd=sci_mjd, expnum=sci_expnum)